In the Season 2 premiere, Shaun's proposed treatment for a homeless patient puts him and Jared in Andrews' crosshairs. Meanwhile, Claire tries to overcome Melendez's reluctance to do a risky heart operation while Glassman must overcome his personal feelings about his oncologist, Dr. Marina Blaize, and face a difficult decision about his health.

Shaun pushes back against Dr. Melendez in order to treat a gravely ill hospital janitor and deal with the return of Lea; and Dr. Lim risks a lawsuit and her career to help a teenage girl repair the damage caused by an archaic custom. Meanwhile, Dr. Glassman exercises demanding oversight with Dr. Blaize in choosing a doctor for his brain surgery.

Dr. Melendez, Dr. Brown and Dr. Park have given a young married couple two choices about their future: save the wife's life or their future ability to start a family. Meanwhile, when Dr. Lim has to take care of some personal business, she leaves oversight of the emergency room to Dr. Murphy and Dr. Reznick; and Dr. Glassman's post-op recovery leaves him struggling to get the rest he needs for ...

Shaun recalls his own past to help an intellectually disabled teenager face separation from his mother, while Claire is put between an injured teenage rock climber and her worried parents. Meanwhile, Glassman's post-op hallucinations force him to confront a personal tragedy.

A patient suffering from anorexia can't gain the necessary weight needed to survive heart surgery, so Claire suggests they perform an experimental surgery which Melendez strongly opposes. Shaun worries Glassman's refusal to walk the hospital floor will keep him from being discharged and tries to persuade him to ambulate. Meanwhile, Shaun and Lea change the terms of their current relationship.

Shaun and Morgan's indecision could affect a young violinist's future.

Dr. Shaun Murphy and Dr. Morgan Reznick must contend with two brothers who are bargaining over life and death. Meanwhile, Dr. Claire Brown's friend who is dying of cancer asks her for something she doesn't think she can give her; and Dr. Aaron Glassman is dealing with the effects of his treatment.

Dr. Shaun Murphy, Dr. Audrey Lim and Dr. Claire Brown's ER patient is forced to reveal a secret to her husband after their treatment caused a complication. Meanwhile, Dr. Neil Melendez, Dr. Morgan Reznick and Dr. Alex Park struggle with a patient whose parents don't believe in vaccination.

Dr. Neil Melendez, Dr. Morgan Reznick and Dr. Claire Brown grapple with a patient's wish to perform an operation that would keep him from acting on his pedophilic urges; and Dr. Shaun Murphy learns a lesson in empathy.

In the winter finale, Dr. Shaun Murphy and Dr. Alex Park treat two patients who collapse at the local airport and whose symptoms point to an infection that may become airborne. The staff races to contain the infection before it spreads to the rest of the people in the ER, resulting in a hospital quarantine during the holidays.

In the midseason return, the hospital is still in quarantine as Dr. Shaun Murphy continues to be overwhelmed by the chaos and noise in the emergency room; Dr. Morgan Reznick struggles to keep her patients alive, and Dr. Audrey Lim fights for her life. Meanwhile, Dr. Neil Melendez and Dr. Claire Browne must find a way to complete their patient's bone marrow transplant, despite the quarantine.

In the aftermath of the quarantine, the staff of San Jose St. Bonaventure Hospital tries to return to their normal routines as the Department of Public Health office decides they need to review what transpired to restore public confidence. Meanwhile, as Dr. Audrey Lim (Christina Chang) recovers from the virus, she and Dr. Neil Melendez (Nicholas Gonzalez) navigate their new personal and workin...

Dr. Shaun Murphy, Dr. Morgan Reznick and Dr. Audrey Lim treat a woman with autism and a delicate brain condition while navigating the complicated relationship she has with her roommate, who is also on the spectrum. Meanwhile, Lea and Shaun are still figuring out their friendship and roommate status.

Dr. Andrews tries to convince a grieving family to donate their teenage daughters face to another young girl whose face was horribly disfigured in an accident.

Shaun's blunt honesty with a distraught mother of a critically ill newborn baby causes the new chief of surgery to question keeping him on as a resident.

The new chief of surgery, Dr. Jackson Han, believes Dr. Shaun Murphy is a liability more than an asset and works to keep him out of the operating room permanently.

Dr. Shaun Murphy is desperate to join the team on a dangerous procedure involving a patient's tumor removal. However, having been removed by Dr. Jackson Han from the surgery team, he must use his talents to help figure out the cause of an infant's injuries.

As a barroom fight sends Shaun (Freddie Highmore) to seek treatment at St. Bonaventure's, Park and Morgan disagree over an elderly woman's post-operative symptoms. Melendez (Nicholas Gonzalez) and Lim (Christina Chang) make their romance public, while Glassman continues to pursue a relationship with a good friend.